Mutagenetix > Incidental Mutation

Incidental Mutation 'R1565:Rfx1'

175202

Institutional Source

Beutler Lab

Gene Symbol

Rfx1

Ensembl Gene

ENSMUSG00000031706

Gene Name

regulatory factor X, 1 (influences HLA class II expression)

Synonyms

MMRRC Submission

039604-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1565 (G1)

Quality Score

219

Status

Validated

Chromosome

Chromosomal Location

84066834-84096992 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 84073946 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 59 (T59A)

Ref Sequence

ENSEMBL: ENSMUSP00000147677 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000005600] [ENSMUST00000211046]

AlphaFold

P48377

Predicted Effect

probably benign
Transcript: ENSMUST00000005600
AA Change: T59A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000005600
Gene: ENSMUSG00000031706
AA Change: T59A

Domain	Start	End	E-Value	Type
low complexity region	11	47	N/A	INTRINSIC
low complexity region	53	67	N/A	INTRINSIC
low complexity region	73	92	N/A	INTRINSIC
Pfam:RFX1_trans_act	106	176	9.6e-9	PFAM
Pfam:RFX1_trans_act	211	366	1.8e-59	PFAM
Pfam:RFX_DNA_binding	420	498	2.5e-35	PFAM
Blast:HisKA	705	768	3e-28	BLAST
low complexity region	908	920	N/A	INTRINSIC
low complexity region	932	948	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000209362

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000210660

Predicted Effect

probably benign
Transcript: ENSMUST00000211046
AA Change: T59A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.5%
20x: 90.0%

Validation Efficiency

96% (82/85)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has been shown to regulate a wide variety of genes involved in immunity and cancer, including the MHC class II genes and genes that may be involved in cancer progression. This gene exhibits altered expression in glioblastoma and the autoimmune disease systemic lupus erythematosis (SLE). [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a gene trap allele die prior to implantation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810021J22Rik	G	A	11: 58,880,501	G270S	probably benign	Het
Abtb1	T	C	6: 88,836,554	T401A	probably benign	Het
Adamts14	A	T	10: 61,270,897	M148K	probably damaging	Het
Adcy5	A	G	16: 35,268,957	E508G	probably damaging	Het
Ankfy1	T	A	11: 72,757,318	L875H	probably damaging	Het
Cacng3	A	T	7: 122,768,401	D168V	probably damaging	Het
Clpb	G	A	7: 101,785,461	R488Q	probably benign	Het
Cpxm2	A	T	7: 132,062,145	Y350N	probably damaging	Het
D130040H23Rik	T	A	8: 69,303,160	*406R	probably null	Het
Dnah10	T	A	5: 124,829,614	D4236E	probably damaging	Het
Dpf3	T	A	12: 83,370,617	Y27F	probably damaging	Het
Esp4	T	C	17: 40,602,595	*118Q	probably null	Het
Fam222b	T	C	11: 78,154,662	S222P	possibly damaging	Het
Flnc	T	C	6: 29,455,171	V1933A	probably damaging	Het
Gem	T	C	4: 11,713,709	F282L	possibly damaging	Het
Gli2	T	C	1: 118,841,930	T631A	possibly damaging	Het
Gm13088	G	A	4: 143,655,617	Q170*	probably null	Het
Gpld1	T	A	13: 24,956,068	V116E	probably damaging	Het
Gpr176	A	G	2: 118,280,214	M188T	probably benign	Het
Grk5	T	C	19: 61,089,972	V489A	probably damaging	Het
H2-Ke6	C	T	17: 34,027,495	V105I	possibly damaging	Het
Hpdl	T	C	4: 116,820,883	N127S	probably damaging	Het
Id4	G	T	13: 48,262,294	V151L	possibly damaging	Het
Kcnh8	G	T	17: 52,956,881	G802V	probably benign	Het
Lamc1	C	A	1: 153,242,743	S894I	probably benign	Het
Larp1b	A	G	3: 40,972,384	N184S	probably damaging	Het
Lhx1	A	T	11: 84,519,821	S226T	probably benign	Het
Lmo7	A	T	14: 101,887,521	Q472L	probably damaging	Het
Mog	G	C	17: 37,017,582	N152K	possibly damaging	Het
Mttp	A	G	3: 138,116,405		probably null	Het
Mycbp2	A	G	14: 103,252,509	V953A	possibly damaging	Het
Myo3a	A	T	2: 22,340,280	Y509F	probably damaging	Het
Myo9b	A	G	8: 71,315,192	N303S	possibly damaging	Het
Nek3	T	C	8: 22,132,201		probably null	Het
Nlrc4	A	T	17: 74,441,931	D771E	probably benign	Het
Nup160	A	T	2: 90,722,061	N1127I	possibly damaging	Het
Oas1h	A	T	5: 120,862,600	N91I	probably damaging	Het
Olfr1225	A	T	2: 89,170,627	V195D	probably benign	Het
Olfr1226	G	T	2: 89,193,883	S50R	probably damaging	Het
Olfr1342	T	A	4: 118,690,192	N87Y	probably damaging	Het
Parp4	T	C	14: 56,589,872		probably benign	Het
Pi4ka	G	A	16: 17,281,900	C96Y	probably null	Het
Pira2	A	T	7: 3,844,549	F47Y	probably damaging	Het
Pkhd1	C	A	1: 20,347,457	G2490V	probably damaging	Het
Plekhg1	C	T	10: 3,940,526	T394I	probably damaging	Het
Psmd1	T	C	1: 86,091,997		probably benign	Het
Rab3ip	A	T	10: 116,939,223	C77S	probably benign	Het
Reln	A	T	5: 21,925,213	M2700K	probably benign	Het
Ric8b	G	T	10: 84,980,099	V405L	probably benign	Het
Rufy3	G	T	5: 88,640,632	A479S	probably damaging	Het
Sardh	A	T	2: 27,242,719	Y166N	probably damaging	Het
Slamf6	T	G	1: 171,934,408	V132G	possibly damaging	Het
Slc12a3	T	G	8: 94,345,877	H674Q	possibly damaging	Het
Sned1	G	A	1: 93,281,654	V830M	possibly damaging	Het
Srsf9	A	G	5: 115,327,370	N21S	possibly damaging	Het
Stkld1	A	T	2: 26,950,090	T391S	probably benign	Het
Sumf2	C	A	5: 129,859,914	N230K	probably damaging	Het
Tbc1d22a	T	C	15: 86,235,569	V22A	possibly damaging	Het
Thsd7b	T	A	1: 129,596,041	S194T	possibly damaging	Het
Tmem27	A	G	X: 164,118,234	D184G	possibly damaging	Het
Tnn	T	A	1: 160,097,265	Y1173F	probably damaging	Het
Top2a	A	G	11: 99,001,054	F1122L	probably damaging	Het
Trappc9	G	A	15: 73,025,967	R377W	probably damaging	Het
Trim39	G	A	17: 36,268,854	R70W	probably damaging	Het
Ttn	G	A	2: 76,794,261	T15289I	probably damaging	Het
Ugt2b38	A	T	5: 87,411,914	V373E	probably damaging	Het
Usp54	A	G	14: 20,607,159	S24P	probably damaging	Het
Vmn2r27	C	T	6: 124,231,634	G51S	probably benign	Het
Xylt2	C	T	11: 94,667,594	A579T	probably benign	Het
Zbtb21	A	G	16: 97,952,427	S247P	probably benign	Het
Zc3h7b	C	T	15: 81,777,088	P376L	probably benign	Het
Zfp251	T	A	15: 76,853,038	R613S	probably damaging	Het
Zfp251	C	T	15: 76,853,039	R613K	possibly damaging	Het
Zfp91	T	C	19: 12,779,075	D135G	probably benign	Het

Other mutations in Rfx1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01612:Rfx1	APN	8	84092972	critical splice acceptor site	probably null
IGL01779:Rfx1	APN	8	84092662	splice site	probably benign
IGL02505:Rfx1	APN	8	84095809	missense	possibly damaging	0.79
IGL02741:Rfx1	APN	8	84095842	missense	possibly damaging	0.94
R1793:Rfx1	UTSW	8	84066421	unclassified	probably benign
R1808:Rfx1	UTSW	8	84095048	missense	probably damaging	1.00
R1971:Rfx1	UTSW	8	84095497	missense	probably damaging	1.00
R4542:Rfx1	UTSW	8	84090237	missense	probably damaging	1.00
R4690:Rfx1	UTSW	8	84082745	missense	possibly damaging	0.50
R4995:Rfx1	UTSW	8	84080114	splice site	probably null
R5163:Rfx1	UTSW	8	84093211	missense	probably damaging	0.98
R5212:Rfx1	UTSW	8	84066592	unclassified	probably benign
R5227:Rfx1	UTSW	8	84074058	missense	probably damaging	0.99
R5401:Rfx1	UTSW	8	84066376	splice site	probably null
R5431:Rfx1	UTSW	8	84082720	nonsense	probably null
R5584:Rfx1	UTSW	8	84088077	splice site	probably null
R5693:Rfx1	UTSW	8	84073904	missense	unknown
R6210:Rfx1	UTSW	8	84093018	missense	probably damaging	1.00
R6715:Rfx1	UTSW	8	84095815	missense	possibly damaging	0.49
R6920:Rfx1	UTSW	8	84095488	missense	probably damaging	1.00
R7131:Rfx1	UTSW	8	84095079	missense	probably damaging	0.96
R7155:Rfx1	UTSW	8	84094826	missense	probably damaging	0.99
R7336:Rfx1	UTSW	8	84073756	start gained	probably benign
R7467:Rfx1	UTSW	8	84073913	missense	possibly damaging	0.86
R8105:Rfx1	UTSW	8	84087876	missense	possibly damaging	0.92
R8145:Rfx1	UTSW	8	84074028	missense	probably benign	0.06
R8261:Rfx1	UTSW	8	84092850	missense	probably benign	0.00
R8263:Rfx1	UTSW	8	84094854	missense	probably damaging	1.00
R8443:Rfx1	UTSW	8	84079886	missense	probably benign	0.00
R8680:Rfx1	UTSW	8	84091455	missense	possibly damaging	0.82
R9302:Rfx1	UTSW	8	84091033	missense	possibly damaging	0.50
R9473:Rfx1	UTSW	8	84093274	missense	probably damaging	0.96
R9766:Rfx1	UTSW	8	84087747	missense	probably damaging	1.00
Z1177:Rfx1	UTSW	8	84090277	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATGTTACTGAGCTACAGGCAGCCC -3'
(R):5'- GAGATGCCTTGATTCGCTTGCAC -3'

Sequencing Primer
(F):5'- CCACAAGCATcccagcc -3'
(R):5'- ATTCGCTTGCACAGGTAGC -3'

Posted On

2014-04-24